Genome evolution in an agricultural pest following adoption of transgenic crops

Replacing synthetic insecticides with transgenic crops for pest management has been economically and environmentally beneficial, but these benefits erode as pests evolve resistance. It has been proposed that novel genomic approaches could track molecular signals of emerging resistance to aid in resistance management. To test this, we quantified patterns of genomic change in Helicoverpa zea, a major lepidopteran pest and target of transgenic Bacillus thuringiensis (Bt) crops, between 2002 and 2017 as both Bt crop adoption and resistance increased in North America. Genomic scans of wild H. zea were paired with quantitative trait locus (QTL) analyses and showed the genomic architecture of field-evolved Cry1Ab resistance was polygenic, likely arising from standing genetic variation. Resistance to pyramided Cry1A.105 and Cry2Ab2 toxins was controlled by fewer loci. Of the 11 previously described Bt resistance genes, 9 showed no significant change over time or major effects on resistance. We were unable to rule out a contribution of aminopeptidases (apns), as a cluster of apn genes were found within a Cry-associated QTL. Molecular signals of emerging Bt resistance were detectable as early as 2012 in our samples, and we discuss the potential and pitfalls of whole-genome analysis for resistance monitoring based on our findings. This first study of Bt resistance evolution using whole-genome analysis of field-collected specimens demonstrates the need for a more holistic approach to examining rapid adaptation to novel selection pressures in agricultural ecosystems.

LIFE-Seq: A universal Large Integrated DNA Fragment Enrichment Sequencing strategy for transgene integration in genetically modified organisms

Molecular characterisation of genetically modified organisms (GMOs) yields basic information on exogenous DNA integration, including integration sites, entire inserted sequences and structures, flanking sequences and copy number, providing key data for biosafety assessment. However, there are few effective methods for deciphering transgene integration, especially for large DNA fragment integration with complex rearrangement, inversion, and tandem repeats. Herein, we developed a universal Large Integrated DNA Fragments Enrichment strategy combined with PacBio Sequencing (LIFE-Seq) for deciphering transgene integration in GMOs. Universal tilling DNA probes targeting transgenic elements and exogenous genes facilitate specific enrichment of large inserted DNA fragments associated with transgenes from plant genomes, followed by PacBio sequencing. LIFE-Seq were evaluated using six GM events and four crop species. Target DNA fragments averaging ∼6275 bp were enriched and sequenced, generating ∼26,352 high fidelity reads for each sample. Transgene integration structures were determined with high repeatability and sensitivity. Compared with whole-genome sequencing, LIFE-Seq achieved better data integrity and accuracy, greater universality, and lower cost, especially for transgenic crops with complex inserted DNA structures. LIFE-Seq could be applied in molecular characterisation of transgenic crops and animals, and complex DNA structure analysis in genetics research.

Production and Adoption of Transgenic Crops in Sub-Saharan Africa

Food insecurity is high in sub-Saharan Africa. It has been estimated that 29 out of the 40 low income countries and countries with the highest rates of malnutrition are found in this region. Therefore, increasing agriculture productivity in sub-Saharan Africa is a priority and utilization of scientific and technological advances could enhance agricultural productivity. While the use of transgenic crops has been floated as one of the key solutions, to this effect, the region has continuously experience low levels of adoption compared to other regions. This paper reviews the state of production and adoption in sub-Saharan Africa, with an in-depth explanation of factors that may have led to low adoption levels. Furthermore, biosafety measures meant to regulate production and utilization of transgenic crops have also be discussed.

Investigating the status of transgenic crops in Iran in terms of cultivation, consumption, laws and rights in comparison with the world

Recently, there has been a development in transgenic technologies in many countries to meet nutritional needs of increasing worlds҆ population. However, there are some concerns about possible risks in the field of growing genetically modified (GM) food, such as threats of biodiversity and food allergies making their use a challenge. Therefore, the present study was conducted to investigate the economic effects and political scopes of GM foods in production sector and policies made by different countries in the world and Iran. Moreover, essential (practical and legal) solutions and guidelines were provided for production and consumption of GM foods, which are useful for governmental entities, Iranian politicians, and consumers' rights. The latest situation of transgenic crops in the countries with which Iran has the highest exchange of agricultural products (including Turkey, Pakistan, and the European Union (EU)) was also studied. Although, Iran has been one of leading Asian countries not only in the field of transfer of technical knowledge of genetic engineering, but also in development of the specialized knowledge of biosafety, and despite production of several transgenic plant lines by Iranian researchers, unfortunately no GM crop has obtained release and cultivation license except for GM rice that its growing process was banned after change of government. According to findings of this study, in Iran, growing and production process of GM crops does not follow the global trend owing to scientific and legal infrastructures.

Obtaining the rapA1 genome-transformed tomato plants

Bacterial agglutinin RapA1 is involved in the attachment of rhizobia to the roots of macrosymbiont plants. Obtaining transgenic crops that produce this protein directly on the root surface is important for studying the symbiosis of these plants with rhizobia. Tomatoes (Lycopersicon lycopersicum L.) cultivar Gruntovy Gribovskiy 1180 were transformed with the gene rapA1 using the Agrobacterium tumefaciens AGL0 strain carrying the vector pCambia1301LPSLRapA1. The efficiency of the developed transformation method was about 5%.

Controlling transgene flow from engineered crops to unintended hosts by molecular approaches.

For most transgenic crops, the purported ecological risk from transgenic-host hybridization and introgression to unintended host species is negligible. Nonetheless, there remains a risk-associated focus on the potential for gene flow in the governance and regulation of crop biotechnology. Because of uncertainties in the large world of biology as well as regulatory certainties (regulations will likely not diminish), researchers and stakeholders have a great interest in eliminating or substantially decreasing gene flow from transgenic crops. To that end, numerous approaches have been investigated for limiting transgene flow via hybridization and introgression to unintended hosts. While such bioconfinement may be accomplished by ecological and management strategies as discussed elsewhere in this book, this chapter focuses on mitigating unintended gene flow from engineered crops by way of genetic engineering itself. The chapter will mainly discuss the manipulation of relatively simple means to alter plant sexual reproduction and plant growth and development to control transgene flow, with the desired outcome being the prevention of transgenes from moving and/or introgression into free-living unintended hosts. These approaches include: (i) decreasing or delaying flowering; (ii) eliminating pollen production via male sterility or selective male sterility; (iii) removing transgenes from pollen or eggs by gene use restriction technologies; and (iv) kill switches. Emerging synthetic biology approaches that may be used for transgene bioconfinement are explored. Taken together, the same molecular biology strategies that are used to improve crops can also help assure their biosafety.